Commercial shrimp farms suffer extensive losses due to the effects of a number of common pathogens. White Spot Syndrome Virus (WSSV) can cause rapid death in the commercial shrimp, Penaeus monodon. WSSV is a double stranded DNA baculovirus, the complete genome of which has been sequenced (van Hulten et al. Virology 286:7-22 (2001); and Yang et al. J. Virol. 75:11811-11820 (2001)). There are at least 12 variants of WSSV found in Thailand that are distinguished by differences in multiple repeat lengths in open reading frame (ORF) 94.
WSSV spreads rapidly and can devastate a commercial shrimp operation within two weeks. Detection of WSSV in hatchery broodstock and in post-larvae allows infected shrimp to be eliminated before entry into a commercial production system. Consequently, a variety of methods have been developed for the detection of WSSV in shrimp, including nucleic acid-based methods and immunological methods (You et al., Current Topics in Virology 4:63-73 (2004); and Lightner et al., Aquaculture 164(1):201-220 (1998)). Polymerase chain reaction (PCR) methods are of particular interest because they are simple, rapid, and sensitive. PCR methods for the detection of WSSV, which are based on amplifying different diagnostic regions of the genome, have been described (see for example, Kou et al., U.S. Pat. No. 6,190,862; Lee, U.S. Pat. No. 6,872,532; Hameed et al., Aquaculture International 13(5):441-450 (2005); Jian et al., Diseases of Aquatic Organisms 67(1&2):171-176 (2005); and Durand et al., Journal of Fish Diseases 25(7):381-389 (2002)). Additionally, a PCR-based method, specifically the WSSV-232 assay, has been used in the shrimp industry in Thailand. The assay involves detection of WSSV DNA using primers for a target sequence in ORF 21 (Kiatpathomchai et al., J. of Virology Methods 130:79-82 (2005)). However, there have been outbreaks of WSSV infection following testing for WSSV using the WSSV-232 assay which have been attributed to insufficient sensitivity (Kiatpathomchai et al., supra). Clearly, new and more sensitive assays for the detection of WSSV are needed.
All of the above methods are useful for the detection of WSSV; however, they generally suffer from a lack of specificity, sensitivity, or are complex and time consuming. Additionally, because of the high gene mutation rate in the virus, tests directed to different regions of the genome would be useful. Therefore, there is a need for a highly sensitive assay for WSSV that is rapid, accurate and easily used in the field. The stated problem is addressed herein by the discovery of primers based on new portions of the WSSV genome. The primers identified herein can be used in primer directed amplification or nucleic acid hybridization assay methods for the detection of WSSV without the problems associated with previous methodologies.